bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/toplevel_methods/misc.rb

@@ -1,596 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# require 'bioroebe/toplevel_methods/misc.rb'
-# Bioroebe.reverse_sequence(ARGV)
-# Bioroebe.bisulfite_treatment(ARGV)
-# Bioroebe.return_DNA_composition_hash
-# =========================================================================== #
-module Bioroebe
-
-  require 'bioroebe/encoding/encoding.rb'
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-  require 'bioroebe/toplevel_methods/e.rb'
-  require 'bioroebe/toplevel_methods/esystem.rb'
-  require 'bioroebe/toplevel_methods/extract.rb'
-
-  # ========================================================================= #
-  # === Bioroebe.percentage_count_non_DNA_bases_in_this_sequence
-  #
-  # Usage examples:
-  #
-  #   Bioroebe.percentage_count_non_DNA_bases_in_this_sequence('ATCGF')
-  #   Bioroebe.percentage_count_non_DNA_bases_in_this_sequence('ACTNGTGCTYGATRGTAGC', %w( A T G C Y R ))
-  #
-  # ========================================================================= #
-  def self.percentage_count_non_DNA_bases_in_this_sequence(
-      i, array = Bioroebe.return_DNA_nucleotides
-    )
-    n = count_non_DNA_bases_in_this_sequence(i, array)
-    percentage = (n * 100.0 / i.size.to_f)
-    return percentage
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.count_non_DNA_bases_in_this_sequence
-  #
-  # Usage example:
-  #
-  #   Bioroebe.count_non_DNA_bases_in_this_sequence('ATCGF')
-  #
-  # ========================================================================= #
-  def self.count_non_DNA_bases_in_this_sequence(
-      i, array = Bioroebe.return_DNA_nucleotides
-    )
-    i = i.dup
-    array.each {|this_nucleotide|
-      i.delete!(this_nucleotide)
-    }
-    return i.size
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.sequence_based_on_these_restriction_enzymes
-  #
-  # Usage example:
-  #
-  #   x = Bioroebe.sequence_based_on_these_restriction_enzymes(%w( EcoRI SacI KpnI XmaI BamHI XbaI SalI )); 'GAATTCGAGCTCGGTACCCCCGGGGGATCCTCTAGAGTCGAC'
-  #
-  # ========================================================================= #
-  def self.sequence_based_on_these_restriction_enzymes(*i)
-    require 'bioroebe/enzymes/restriction_enzyme.rb'
-    _ = ''.dup
-    i.flatten.each {|this_restriction_enzyme|
-      _ << ::Bioroebe.restriction_sites?(this_restriction_enzyme)
-    }
-    return _
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.create_jar_archive
-  #
-  # This method will create a .jar file.
-  #
-  # To invoke it from the commandline do:
-  #
-  #   bioroebe --jar
-  #
-  # To execute a .jar file do:
-  #
-  #   java -jar foobar.jar
-  #
-  # ========================================================================= #
-  def self.create_jar_archive
-    e 'Creating a .jar archive next:'
-    e
-    original_dir = return_pwd
-    cd '/home/x/programming/ruby/src/bioroebe/lib/bioroebe/java/bioroebe/src/main/java/'
-    esystem 'jar cf bioroebe.jar bioroebe/'
-    target_file = File.absolute_path('bioroebe.jar')
-    cd original_dir
-    if File.exist? target_file
-      e 'Moving the created .jar file into the current working '\
-        'directory next.'
-      move_file(target_file, original_dir)
-      e 'It should now be at:'
-      e
-      e sfile("  #{original_dir}#{File.basename(target_file)}")
-      e
-    end
-#   esystem 'jar cfe bioroebe.jar myClass myClass.class'
-    e
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.frequency_per_thousand
-  #
-  # The input to this method should be a String ideally. If an Array is
-  # input then it will simply be .join()-ed.
-  #
-  # This method will return a String, if all goes well.
-  # ========================================================================= # 
-  def self.frequency_per_thousand(i)
-    result = "fields: [triplet] [frequency: per thousand] ([number])\n".dup # This String will be returned.
-    if i.is_a? Array
-      i = i.join
-    end
-    i.delete!("\n")
-    hash = ::Bioroebe.codon_frequency_of_this_string(i)
-    hash.default = 0
-    total_n_elements = hash.values.sum
-    append_this = <<-EOF 
-
-UUU#{thousand_percentage(hash['UUU'], total_n_elements)}(     #{hash['UUU']})  UCU#{thousand_percentage(hash['UCU'], total_n_elements)}(     #{hash['UCU']})  UAU#{thousand_percentage(hash['UAU'], total_n_elements)}(     #{hash['UAU']})  UGU#{thousand_percentage(hash['UGU'], total_n_elements)}(     #{hash['UGU']})
-UUC#{thousand_percentage(hash['UUC'], total_n_elements)}(     #{hash['UUC']})  UCC#{thousand_percentage(hash['UCC'], total_n_elements)}(     #{hash['UCC']})  UAC#{thousand_percentage(hash['UAC'], total_n_elements)}(     #{hash['UAC']})  UGC#{thousand_percentage(hash['UGC'], total_n_elements)}(     #{hash['UGC']})
-UUA#{thousand_percentage(hash['UUA'], total_n_elements)}(     #{hash['UUA']})  UCA#{thousand_percentage(hash['UCA'], total_n_elements)}(     #{hash['UCA']})  UAA#{thousand_percentage(hash['UAA'], total_n_elements)}(     #{hash['UAA']})  UGA#{thousand_percentage(hash['UGA'], total_n_elements)}(     #{hash['UGA']})
-UUG#{thousand_percentage(hash['UUG'], total_n_elements)}(     #{hash['UUG']})  UCG#{thousand_percentage(hash['UCG'], total_n_elements)}(     #{hash['UCG']})  UAG#{thousand_percentage(hash['UAG'], total_n_elements)}(     #{hash['UAG']})  UGG#{thousand_percentage(hash['UGG'], total_n_elements)}(     #{hash['UGG']})
-
-CUU#{thousand_percentage(hash['CUU'], total_n_elements)}(     #{hash['CUU']})  CCU#{thousand_percentage(hash['CCU'], total_n_elements)}(     #{hash['CCU']})  CAU#{thousand_percentage(hash['CAU'], total_n_elements)}(     #{hash['CAU']})  CGU#{thousand_percentage(hash['CGU'], total_n_elements)}(     #{hash['CGU']})
-CUC#{thousand_percentage(hash['CUC'], total_n_elements)}(     #{hash['CUC']})  CCC#{thousand_percentage(hash['CCC'], total_n_elements)}(     #{hash['CCC']})  CAC#{thousand_percentage(hash['CAC'], total_n_elements)}(     #{hash['CAC']})  CGC#{thousand_percentage(hash['CGC'], total_n_elements)}(     #{hash['CGC']})
-CUA#{thousand_percentage(hash['CUA'], total_n_elements)}(     #{hash['CUA']})  CCA#{thousand_percentage(hash['CCA'], total_n_elements)}(     #{hash['CCA']})  CAA#{thousand_percentage(hash['CAA'], total_n_elements)}(     #{hash['CAA']})  CGA#{thousand_percentage(hash['CGA'], total_n_elements)}(     #{hash['CGA']})
-CUG#{thousand_percentage(hash['CUG'], total_n_elements)}(     #{hash['CUG']})  CCG#{thousand_percentage(hash['CCG'], total_n_elements)}(     #{hash['CCG']})  CAG#{thousand_percentage(hash['CAG'], total_n_elements)}(     #{hash['CAG']})  CGG#{thousand_percentage(hash['CGG'], total_n_elements)}(     #{hash['CGG']})
-
-AUU#{thousand_percentage(hash['AUU'], total_n_elements)}(     #{hash['AUU']})  ACU#{thousand_percentage(hash['ACU'], total_n_elements)}(     #{hash['ACU']})  AAU#{thousand_percentage(hash['AAU'], total_n_elements)}(     #{hash['AAU']})  AGU#{thousand_percentage(hash['AGU'], total_n_elements)}(     #{hash['AGU']})
-AUC#{thousand_percentage(hash['AUC'], total_n_elements)}(     #{hash['AUC']})  ACC#{thousand_percentage(hash['ACC'], total_n_elements)}(     #{hash['ACC']})  AAC#{thousand_percentage(hash['AAC'], total_n_elements)}(     #{hash['AAC']})  AGC#{thousand_percentage(hash['AGC'], total_n_elements)}(     #{hash['AGC']})
-AUA#{thousand_percentage(hash['AUA'], total_n_elements)}(     #{hash['AUA']})  ACA#{thousand_percentage(hash['ACA'], total_n_elements)}(     #{hash['ACA']})  AAA#{thousand_percentage(hash['AAA'], total_n_elements)}(     #{hash['AAA']})  AGA#{thousand_percentage(hash['AGA'], total_n_elements)}(     #{hash['AGA']})
-AUG#{thousand_percentage(hash['AUG'], total_n_elements)}(     #{hash['AUG']})  ACG#{thousand_percentage(hash['ACG'], total_n_elements)}(     #{hash['ACG']})  AAG#{thousand_percentage(hash['AAG'], total_n_elements)}(     #{hash['AAG']})  AGG#{thousand_percentage(hash['AGG'], total_n_elements)}(     #{hash['AGG']})
-
-GUU#{thousand_percentage(hash['GUU'], total_n_elements)}(     #{hash['GUU']})  GCU#{thousand_percentage(hash['GCU'], total_n_elements)}(     #{hash['GCU']})  GAU#{thousand_percentage(hash['GAU'], total_n_elements)}(     #{hash['GAU']})  GGU#{thousand_percentage(hash['GGU'], total_n_elements)}(     #{hash['GGU']})
-GUC#{thousand_percentage(hash['GUC'], total_n_elements)}(     #{hash['GUC']})  GCC#{thousand_percentage(hash['GCC'], total_n_elements)}(     #{hash['GCC']})  GAC#{thousand_percentage(hash['GAC'], total_n_elements)}(     #{hash['GAC']})  GGC#{thousand_percentage(hash['GGC'], total_n_elements)}(     #{hash['GGC']})
-GUA#{thousand_percentage(hash['GUA'], total_n_elements)}(     #{hash['GUA']})  GCA#{thousand_percentage(hash['GCA'], total_n_elements)}(     #{hash['GCA']})  GAA#{thousand_percentage(hash['GAA'], total_n_elements)}(     #{hash['GAA']})  GGA#{thousand_percentage(hash['GGA'], total_n_elements)}(     #{hash['GGA']})
-GUG#{thousand_percentage(hash['GUG'], total_n_elements)}(     #{hash['GUG']})  GCG#{thousand_percentage(hash['GCG'], total_n_elements)}(     #{hash['GCG']})  GAG#{thousand_percentage(hash['GAG'], total_n_elements)}(     #{hash['GAG']})  GGG#{thousand_percentage(hash['GGG'], total_n_elements)}(     #{hash['GGG']})
-EOF
-    result << append_this
-    return result
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.codon_frequency_of_this_string
-  #
-  # The input to this method should ideally be a String. It will be assumed
-  # to be a RNA string, e. g. mRNA. Thus, all T are replaced with U by
-  # default. This can be toggled via the second argument of this method.
-  #
-  # This method will return a Hash.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.codon_frequency_of_this_string
-  #   Bioroebe.codon_frequency_of_this_string 'ATTCGTACGATCGACTACTACT' # => {"UAC"=>2, "GAC"=>1, "AUC"=>1, "ACG"=>1, "CGU"=>1, "AUU"=>1}
-  #
-  # ========================================================================= #
-  def self.codon_frequency_of_this_string(
-      i = 'ATTCGTACGATCGACTGACTGACAGTCATTCGTAGTACGATCGACTGACTGACAGTCATTCGTAC'\
-          'GATCGACTGACTGACAAGTCATTCGTACGATCGACTGACTTGACAGTCATAA',
-      automatically_convert_into_a_RNA_sequence = true
-    )
-    i = i.join if i.is_a? Array
-    if automatically_convert_into_a_RNA_sequence
-      i = i.dup if i.frozen?
-      i.tr!('T','U')
-    end
-    scanned = i.scan(/.../)
-    tally = scanned.tally
-    # ======================================================================= #
-    # We still have to sort it.
-    # ======================================================================= #
-    sorted_hash = Hash[tally.sort_by {|key, value| value }.reverse]
-    return sorted_hash
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.thousand_percentage
-  #
-  # This method is solely a helper-method for Bioroebe.frequency_per_thousand().
-  # ========================================================================= #
-  def self.thousand_percentage(
-      this_codon_n_times =   1,
-      total_n_elements  = 1000
-    )
-    result = (
-      (this_codon_n_times * 1000.0) / total_n_elements.to_f
-    ).round(1)
-    padded_result = result.to_s.rjust(5, ' ')
-    return padded_result
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.align_this_string_via_multiple_sequence_alignment
-  #
-  # This method will simply return an Array.
-  # ========================================================================= #
-  def self.align_this_string_via_multiple_sequence_alignment(
-      this_string =
-        "PSRARRDAVG--DH--PAVEALP----PQSGPHKKEISFFTVRKEEAADADLWFPS
-         PGGASK--VGQTDNDPQAIKDLP----PQGED------------------------
-        "
-    )
-    if this_string.is_a? Array
-      this_string = this_string.join("\n")
-    end
-    this_string = this_string.dup if this_string.frozen?
-    this_string.strip!
-    this_string.delete!(' ')
-    splitted = this_string.split("\n")
-    return splitted
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.quaternary_encoding_translate_from_alphabet_string_into_the_corresponding_DNA_sequence
-  #
-  # Usage example:
-  #
-  #   Bioroebe.quaternary_encoding_translate_from_alphabet_string_into_the_corresponding_DNA_sequence('OTTO')
-  #
-  # ========================================================================= #
-  def self.quaternary_encoding_translate_from_alphabet_string_into_the_corresponding_DNA_sequence(
-      this_string = 'Hello world'
-    )
-    _ = ''.dup
-    chars = this_string.chars
-    chars.each {|this_char|
-      case chars
-      when ' ','!','?'
-        # pass through in this case.
-      else
-        this_char = this_char.upcase
-        _ << Bioroebe.quaternary_encoding_letter_to_number(this_char)
-      end
-    }
-    return _
-  end
-  
-  # ========================================================================= #
-  # === Bioroebe.quaternary_encoding_DNA_to_numbers
-  #
-  # You can pass in another hash as the second argument to this method,
-  # if you'd like to.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.quaternary_encoding_DNA_to_numbers('TACATCTTTCGATCGATCGG') # => "10201211123012301233"
-  #
-  # ========================================================================= #
-  def self.quaternary_encoding_DNA_to_numbers(
-      i    = 'TACATCTTTCGATCGATCGG',
-      hash = { A: 0, T: 1, C: 2, G: 3 }
-    )
-    i = i.chars unless i.is_a? Array
-    return i.map {|entry|
-      hash[entry.to_sym]
-    }.join
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.quaternary_encoding_letter_to_number
-  # ========================================================================= #
-  def self.quaternary_encoding_letter_to_number(
-    letter,
-    use_this_hash = {
-      '0000': :A,
-      '1000': :B,
-      '2000': :C,
-      '3000': :D,
-      '0100': :E,
-      '0200': :F,
-      '0300': :G,
-      '0010': :H,
-      '0020': :I,
-      '0030': :J,
-      '0001': :K,
-      '0002': :L,
-      '0003': :M,
-      '1100': :N,
-      '1200': :O,
-      '1300': :P,
-      '1110': :Q,
-      '1120': :R,
-      '1130': :S,
-      '1210': :T,
-      '1220': :U,
-      '1230': :V,
-      '1231': :W
-    })
-    use_this_hash = use_this_hash.invert
-    return use_this_hash[letter.to_sym].to_s
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.quaternary_encoding_number_to_letter
-  # ========================================================================= #
-  def self.quaternary_encoding_number_to_letter(
-    number,
-    use_this_hash = {
-      '0000': :A,
-      '1000': :B,
-      '2000': :C,
-      '3000': :D,
-      '0100': :E,
-      '0200': :F,
-      '0300': :G,
-      '0010': :H,
-      '0020': :I,
-      '0030': :J,
-      '0001': :K,
-      '0002': :L,
-      '0003': :M,
-      '1100': :N,
-      '1200': :O,
-      '1300': :P,
-      '1110': :Q,
-      '1120': :R,
-      '1130': :S,
-      '1210': :T,
-      '1220': :U,
-      '1230': :V,
-      '1231': :W
-    })
-    return use_this_hash[number.to_s].to_s
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.quaternary_encoding_numbers_to_DNA
-  # ========================================================================= #
-  def self.quaternary_encoding_numbers_to_DNA(
-      i    = '10201211123012301233',
-      hash = { A: 0, T: 1, C: 2, G: 3 }
-    )
-    i = i.chars unless i.is_a? Array
-    inverted_hash = hash.invert
-    return i.map {|number|
-      inverted_hash[number.to_i]
-    }.join
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.download_human_genome
-  # ========================================================================= #
-  def self.download_human_genome(
-      from_this_URL = 'https://bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz'
-    )
-    esystem "wget #{from_this_URL}"
-    extract(
-      File.basename(from_this_URL)
-    )
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.guess_format
-  # ========================================================================= #
-  def self.guess_format(i)
-    case i
-    # ======================================================================= #
-    # === fasta
-    # ======================================================================= #
-    when /.fa$/,
-         /.fna$/,
-         /.faa$/,
-         /.fasta$/
-      'fasta'
-    # ======================================================================= #
-    # === fastq
-    # ======================================================================= #
-    when /.fq$/,
-         /.fastq$/
-      'fastq'
-    when /.fx/
-      ''
-    end
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.return_ubiquitin_sequence
-  #
-  # This method will simply return the Ubiquitin sequence. We may also
-  # colourize some aminoacids, if we have enabled this.
-  # ========================================================================= #
-  def self.return_ubiquitin_sequence(
-      i = 'MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG'
-    )
-    colourize_aa(i) # Consider colourizing it.
-  end; self.instance_eval { alias ubiquitin return_ubiquitin_sequence } # === Bioroebe.ubiquitin
-
-  # ========================================================================= #
-  # === Bioroebe.reverse_sequence
-  # ========================================================================= #
-  def self.reverse_sequence(i)
-    i = i.first if i.is_a? Array
-    i.reverse
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.bisulfite_treatment
-  #
-  # Simply convert all C into U. The underlying idea here is that
-  # bilsufite will convert unmethylated Cytosines into Uracil.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.bisulfite_treatment('CCCGCAATGCATACCTCGCCG') # => "UUUGUAATGUATAUUTUGUUG"
-  #
-  # ========================================================================= #
-  def self.bisulfite_treatment(i)
-    if i.is_a? Array
-      i = i.join('').strip
-    end
-    i.tr('C','U')
-  end; self.instance_eval { alias bisulfie bisulfite_treatment } # === Bioroebe.bisulfite
-
-  # ========================================================================= #
-  # === Bioroebe.batch_create_windows_executables
-  #
-  # This method is only useful for windows. We will use "ocra" to create
-  # various .exe files that have the desired widgt-functionality.
-  #
-  # Note that the functionality depends on the roebe-gem.
-  # ========================================================================= #
-  def self.batch_create_windows_executables
-    begin
-      require 'roebe/custom_methods/custom_methods.rb'
-    rescue LoadError; end
-    array_these_files =  %w(
-      /home/x/programming/ruby/src/bioroebe/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb
-    )
-    array_these_files.each {|this_file|
-      Roebe.ocra_build(
-        this_file,
-        File.basename(this_file).delete_suffix('.rb')
-      )
-    }
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.create_the_pdf_tutorial
-  #
-  # This method can be used to quickly turn the README.md file into
-  # a .pdf file, for whatever the reason the user may want this.
-  # ========================================================================= #
-  def self.create_the_pdf_tutorial(
-      read_from_this_file = '/home/x/programming/ruby/src/bioroebe/README.md',
-      store_where         = '/Depot/j/example.pdf'
-    )
-
-    require 'prawn'
-
-    Prawn::Fonts::AFM.hide_m17n_warning = true # Hide a useless warning.
-
-    pdf = Prawn::Document.new(
-            page_size: 'A4',
-            page_layout: :landscape
-          )
-    pdf.text "The Bioroebe Project", size: 80
-    pdf.start_new_page
-    pdf.bounding_box [50, 600], width: 200 do
-      pdf.fill_color '000000'
-      pdf.text "making bioinformatics great again:", size: 15
-    end
-    pdf.start_new_page
-    dataset = File.read(read_from_this_file, encoding: UTF_ENCODING)
-    dataset = dataset.encode("Windows-1252", invalid: :replace, undef: :replace)
-
-    pdf.text(dataset)
-    e 'Storing at this location: '+store_where
-    pdf.render_file store_where
-  end; self.instance_eval { alias pdf create_the_pdf_tutorial } # === Bioroebe.pdf
-
-  # ========================================================================= #
-  # === Bioroebe.return_DNA_composition_hash
-  # ========================================================================= #
-  def self.return_DNA_composition_hash(
-      of_this_sequence
-    )
-    of_this_sequence = of_this_sequence.first if of_this_sequence.is_a? Array
-    hash = {}
-    array1 = %w( A T C G )
-    array2 = Array.new(array1.size, 0)
-    array = array1.zip(array2) # Zip it up with 0-values here.
-    hash = Hash[array]
-    of_this_sequence.chars.each {|this_char|
-      hash[this_char] += 1
-    }
-    sorted_hash = Hash[*hash.sort_by {|key, value|
-      key
-    }.flatten]
-    # ======================================================================= #
-    # The hash may then look like this:
-    #
-    #   {"A"=>7, "T"=>6, "C"=>7, "G"=>6}
-    #
-    # ======================================================================= #
-    return sorted_hash
-  end
-
-  # ========================================================================= #
-  # === Bioroebe.windows_platform?
-  # ========================================================================= #
-  def self.windows_platform?
-    case RUBY_PLATFORM
-    when /(?:mswin|bccwin|mingw|windows)(?:32|64)/i
-      true
-    else
-      false
-    end
-  end; self.instance_eval { alias on_windows?    windows_platform? } # === Bioroebe.on_windows?
-       self.instance_eval { alias is_on_windows? windows_platform? } # === Bioroebe.is_on_windows?
-
-  # ========================================================================= #
-  # === Bioroebe.two_dimensional_plot
-  #
-  # This method makes use of gnuplot to draw a 2D plot.
-  #
-  # The first argument should contain your dataset, as a String.
-  # ========================================================================= #
-  def self.two_dimensional_plot(
-      dataset =  '6 12
-8 14
-10 18
-12 23
-14 28
-16 29
-18 26
-20 23
-22 20',
-      optional_hash = {
-        width:    800,
-        height:   640
-      }
-    )
-    # ======================================================================= #
-    # Provide some generic fall-back values for width and height next:
-    # ======================================================================= #
-    width  = 1000
-    height =  800
-    _ = optional_hash
-    if _.is_a? Hash
-      # ===================================================================== #
-      # === :width
-      # ===================================================================== #
-      if _.has_key? :width
-        width = _.delete(:width)
-      end
-      # ===================================================================== #
-      # === :height
-      # ===================================================================== #
-      if _.has_key? :height
-        height = _.delete(:height)
-      end
-    end
-    # ======================================================================= #
-    # Go to a safe base directory.
-    # ======================================================================= #
-    cd :bioroebe_log_directory
-    mkdir 'gnuplot' unless File.directory?('gnuplot')
-    cd 'gnuplot'
-    # ======================================================================= #
-    # First save the dataset into dataset.md:
-    # ======================================================================= #
-    into = File.absolute_path('dataset.md')
-    e 'Storing the dataset into '+sfile(into)+' next.'
-    write_what_into(dataset, into)
-    what = <<-EOF
-
-set terminal png size #{width},#{height} enhanced font "Helvetica, 18"
-set output 'fancy_graph.png'
-plot '#{into}' with linespoints ls 1 notitle
-
-EOF
-    into = File.absolute_path('gnuplot.file')
-    e 'Storing into '+into+'.'
-    write_what_into(what, into)
-    esystem 'gnuplot '+into
-    if File.exist? 'fancy_graph.png' and is_on_roebe?
-      Open.in_browser('fancy_graph.png')
-    end
-  end
-
-end
-
-if __FILE__ == $PROGRAM_NAME
-  puts Bioroebe.reverse_sequence(ARGV)
-  puts Bioroebe.bisulfite_treatment('CCCGCAATGCATACCTCGCCG')
-  puts Bioroebe.return_ubiquitin_sequence
-  pp Bioroebe.return_DNA_composition_hash(ARGV)
-end # rb misc ATGC # => CGTA
-    # rb misc.rb GATCTGCAGTACGTACGTACTGACAC
-    # returnubiquitinsequence